When I forced the second HVR-3000 to operate as the primary card it was clear as a bell, and the picture smooth. It was only then I twigged to the fact that the layout of this particular motherboard puts the PCI-Ex videocard's processor etc about 5mm (or less) from the tuner circuitry on the HVR-3000 in the No1 PCI slot. And that the No1 HVR-3000 screens the No2 HVR-3000 (in PCI slot 2 right next door) from the video card. To test the theory that EM interference from the videocard was the issue I built an EM shield by sandwiching tinfoil between two layers of insulating plastic and placing it between the videocard and the No1 HVR-3000 (being careful about cooling flows). And the interference vanished.
So I post this as a word of warning to potential HTPC builders. Look carefully at the location of PCI-Ex and PCI slots if you are going the multi-tuner route. The M2A-VM HDMI is a micro-ATX board with the slots all close together, and with the benefit of hindsight an ATX board may have been a better bet (like an idiot I bought a 'nice' looking case first - for WAF - only to realise it was a micro-ATX, which limited my choices from then on).